Skip to Main content Skip to Navigation
Conference papers

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data

Gustavo Akio Tominaga Sacomoto 1 Vincent Lacroix 1 Marie-France Sagot 1, *
* Corresponding author
1 BAMBOO - An algorithmic view on genomes, cells, and environments
LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558, Inria Grenoble - Rhône-Alpes
Abstract : We present a new algorithm for enumerating bubbles with length constraints in directed graphs. This problem arises in transcriptomics, where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced by RNA-seq. This is the fi rst polynomial-delay algorithm for this problem and we show that in practice, it is faster than previous approaches. This enables us to deal with larger instances and therefore to discover novel alternative splicing events, especially long ones, that were previously overseen using existing methods.
Complete list of metadata

https://hal.inria.fr/hal-00842982
Contributor : Marie-France Sagot <>
Submitted on : Wednesday, July 10, 2013 - 7:05:20 AM
Last modification on : Tuesday, July 20, 2021 - 5:20:04 PM

Identifiers

  • HAL Id : hal-00842982, version 1

Collections

Citation

Gustavo Akio Tominaga Sacomoto, Vincent Lacroix, Marie-France Sagot. A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data. Workshop on Algorithms in Bioinformatics (WABI), Sep 2013, Nice, France. ⟨hal-00842982⟩

Share

Metrics

Record views

368